Fig. 6

Transcriptomics confirm the delay in differentiation of human RFX2 -/- LUHMES neurons. See also Additional file 2: Fig. S3-S5. A Principal component analysis of 78 (41 WT and 37 RFX2 -/-) LUHMES STRT RNA-seq time course samples, representing the process of neuron differentiation from d0 to d6. Numbers represent the days and arrows connect the neighboring days. B Similarity heat map of SingleR annotation scores of different types of human fetal midbrain cells and neurons [48] using the 78 LUHMES WT and RFX2 -/- samples as reference. Note the apparent differentiation delay of RFX2 -/-, visible in the comparisons to differentiating neuronal cell types (d1/d2-d6,upper right corner), while in the comparisons to precursor cell types (d0; middle left) no differences between WT and RFX2 -/- are apparent. C Left: Scaled expression profile of 1,574 genes downregulated in RFX2 -/- LUHMES STRT RNA-seq samples (Cluster 3) throughout the differentiation time course. 3,476 genes with a significantly variable expression between WT and RFX2 -/- throughout the time course were clustered into three clusters based on their expression patterns during the differentiation process. Lines are local polynomial regression fittings of the scaled expression of the genes in each cluster, depicted in blue (WT) and in red (RFX2 -/-). Right: Gene ontology (GO) enrichment analysis of these 1,574 genes in Cluster 3. The red dashed line represents the adjusted p-value = 0.05. Clusters 1–3 are depicted side-by-side in Additional file 2: Fig. S3. D Transcription factor binding motif enrichment analysis of significantly downregulated transcript far 5’ ends (TFEs) in RFX2 -/- LUHMES STRT RNA-seq samples at day 2 and day 3: only the top five significantly enriched motifs are listed. The complete transcription factor binding motif enrichment analysis throughout the time course of neuron differentiation and maturation (d0-d6) is shown in Additional file 2: Fig. S5